The Y chromosome is unusual in being constitutively haploid and escaping recombination for most of its length. This has led to a correspondingly unusual genomic landscape, rich in segmental duplications, which provide a potent environment for the generation of copy number variation (CNV). Interest in the chromosome comes from diverse fields, including infertility research, population genetics, forensics, and genealogy. Together with inclusion in more systematic surveys, this has led to the ascertainment of a variety of CNVs. Assessment in the context of the well-resolved Y phylogeny allows their mutational history to be deciphered and an estimation of mutation rate. The functional consequences of variants are moderated by the specialization of the chromosome and the presence of functionally equivalent X-chromosomal homologues for some genes. However, deletions of the AZFa, b, and c regions cause impaired spermatogenesis, while partial deletions and duplications within these regions, and deletions and duplications elsewhere, may be selectively neutral or have subtle phenotypes.

This is the author's final draft of the paper published as Cytogenetic and Genome Research, 2009, 123 (1-4), pp. 253-262. The final version is available from http://content.karger.com/ProdukteDB/produkte.asp?doi=10.1159/000184715. Doi: 10.1159/000184715